Ten quick tips to SNIFF out sustainable and secure scientific software journals.plos.org/ploscompbiol... 🧬💻🧪

This was a fun one to write. Partly because of the subject, mostly because of the @uvadatascience.bsky.social people I wrote it with 🧑‍💻 blog.stephenturner.us/p/how-to-sni...

DIAMOND v2.2.4 is available today, providing compositional matrix adjust for the clustering workflows and more. github.com/bbuchfink/di...

New study by Alexander Henoch (@ahenoch.bsky.social), a PhD student in our group @hifmb.de and @awi.de, shows what it takes to bring gene synteny into microbial pangenomes, and what we learn about the variability landscape of genomes when we do that. See the pre-print here: doi.org/10.64898/202...

Few people know that BLASTP applies SEG masking to the target sequences by default github.com/bbuchfink/di...

OrthoFinder v3: a tool for phylogenetic orthology inference with boosted accuracy and scalability for massive datasets. @lauriebelch.bsky.social @stevenkelly.bsky.social @jonathancholmes.bsky.social @yiliu88.bsky.social www.nature.com/articles/s41...

The new OrthoFinder paper is out now! In this new work, we introduce major advances in accuracy and scalability, allowing analysis on much larger datasets www.nature.com/articles/s41... github.com/OrthoFinder/...

Sandpiper 2 is up. 913,000 metagenomic community profiles w @ace-gtdb.bsky.social R232, 200k more than 1.0. sandpiper.qut.edu.au GlobDB coming. Thanks to @aroneys.bsky.social @thepatientwait.bsky.social @iambrettb.bsky.social and especially the new kid @nhstefan.bsky.social

This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated," www.npr.org/2026/05/21/n...

Honored to announce that DIAMOND is one of 52 benchmarks in SPEC CPU®2026 🥳🎉🥂https://arxiv.org/abs/2605.01575

This is now published in Genome Research (doi.org/10.1101/gr.2...). Thank you everyone for your feedback and also the anonymous reviewers who helped to greatly improve the paper. I hope this becomes a useful resource for the community.

Tiberius 2.0.0 is out 🎉 Now supports 7 eukaryotic clades, covering ~92% of NCBI assemblies. Modular rewrite + ~30% faster runtime. Benchmarks included, more soon. Thanks to Lars Gabriel, Richard Krieg & Felix Becker 🙌 github.com/Gaius-August... #bioinformatics #genomics #genomeannotation

Me coding using Claude and Codex @anthropic.com @openaibot.bsky.social

GALBA2 walks into the arena. We rewrote our protein-based genome annotation pipeline in Snakemake. Give it a genome + proteins from close relatives → get gene predictions. No RNA-Seq, no GeneMark needed. miniprot → AUGUSTUS, fully containerised, HPC-ready. github.com/Gaius-Augustus/GALBA2

1/ BRAKER4 hatched! The Earth BioGenome Project is on track to sequence ~1.5M eukaryotic species. Every one needs a structural annotation. No Perl monolith was going to survive that. So we rewrote BRAKER from the ground up. github.com/Gaius-August...

I'm not looking forward to a future where all the tools are being vibe-rewritten into languages people don't want to learn. Who will maintain all this? The original maintainers won't. It's not the language they were comfortable with. Does the prompter understand the tool well enough?

DIAMOND DeepClust: an ultrafast clustering method for organizing the protein universe of life. www.nature.com/articles/s41...

Clustering proteins using DIAMOND is out now @natmethods.nature.com www.nature.com/articles/s41...

NCBI nr database hits 1 billion sequences 🤩

We just released #anvio v9, "eunice" 🎉 This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176. Read the release notes: github.com/merenlab/anv... Visit our up-to-date web page: anvio.org

The 2026 Workshop on Genomics comes to an end! It has been two intense and inspiring weeks of Genomics in Český Krumlov. We hope everyone is going back home with a renewed excitement for science and new friends and collaborations around the world! 🙆🏻‍♀️🧬 #evomics2026

Sequence alignment lecture at the Town Theatre this morning! 🧬💻💎 #evomics2026

DIAMOND v2.1.17 has new output fields sRANK to print taxonomy nodes of the given rank associated with the subject sequence, where RANK can be any rank in the NCBI taxonomy, e.g. sdomain, skingdom, sphylum, sorder, sgenus, sspecies, etc. github.com/bbuchfink/di...

I knew early on I wanted to work with computers, but because of dyslexia I ended up in a lower-tier German school. The career office said a tech job wasn’t realistic. I ignored that, took a convoluted path into university, discovered bioinformatics, got hooked on algorithms&proteins, and became a PI

DIAMOND v2.1.15 now supports all taxonomy features for BLAST databases, and support for using BLAST databases has also been added to the Bioconda version github.com/bbuchfink/di...

www.nature.com/articles/s41... #microsky #microbiome

Ragnarok: a flexible and RApid GeNe Annotation (ROcKs) pipeline deployed through Nextflow https://www.biorxiv.org/content/10.1101/2025.10.03.680343v1

Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper. #Metagenomics #MicrobialCommunities #Bioinformatics @natbiotech.nature.com 🧬 🖥️ www.nature.com/articles/s41...

TaxTriage: An Open-Source Metagenomic Sequencing Data Analysis Pipeline Enabling Putative Pathogen Detection. #Metagenomics #Sequencing #PathogenDetection #Bioinformatics @biorxiv-bioinfo.bsky.social www.biorxiv.org/content/10.1...

OrthoFinder just dropped a major update It’s faster, more accurate, and ready for thousands of genomes Let’s break it down (1/10) github.com/OrthoFinder/... www.biorxiv.org/content/10.1...

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

DIAMOND v2.1.12 provides support for the new NCBI taxonomic ranks and various other fixes. github.com/bbuchfink/di...

Industry friends, now is the time for MUCH more speaking out on behalf of academic colleagues under duress. Here are core open source methods that many of your products doubtlessly depend on either directly or indirectly (see en.wikipedia.org/wiki/HMMER) being abruptly defunded. Make noise.

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

NIH just early-expired its 1st & only software NOFO: “Building Sustainable Software Tools for Open Science.” Our proposal supported lab automation software infrastructure, with backing from major robotics companies. I guess “sustainable” is too risky now. So much for funding the STEM workforce.

DIAMOND v2.1.11 is now available, providing numerous improvements and fixes. github.com/bbuchfink/di...